SMTL ID : 6np0.1

Cryo-EM structure of 5HT3A receptor in presence of granisetron

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: N.191, I.192, T.193, F.223 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain B: N.191, I.192, T.193, F.223 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain C: N.191, I.192, T.193, F.223 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain D: N.191, I.192, T.193, F.223 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain E: N.191, I.192, T.193, F.223 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain A: N.175, E.218, F.220, Y.240, I.242 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain B: N.175, E.218, F.220, Y.240, I.242 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain C: N.175, E.218, F.220, Y.240, I.242 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain D: N.175, E.218, F.220, Y.240, I.242 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: N.175, E.218, F.220, Y.240, I.242 No protein-ligand interaction detected (PLIP)

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.11: 2 residues within 4Å: Chain A: N.109 Ligands: NAG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.109 NAG.12: 1 residues within 4Å: Ligands: NAG.11 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain B: N.109 Ligands: NAG.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.109 NAG.16: 1 residues within 4Å: Ligands: NAG.15 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain C: N.109 Ligands: NAG.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.109 NAG.19: 1 residues within 4Å: Ligands: NAG.18 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain D: N.109 Ligands: NAG.22 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.109 NAG.22: 1 residues within 4Å: Ligands: NAG.21 No protein-ligand interaction detected (PLIP) NAG.25: 2 residues within 4Å: Chain E: N.109 Ligands: NAG.26 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.109 NAG.26: 1 residues within 4Å: Ligands: NAG.25 No protein-ligand interaction detected (PLIP)

5 x CWB: 1-methyl-N-[(1R,5S)-9-methyl-9-azabicyclo[3.3.1]nonan-3-yl]indazole-3-carboxamide

CWB.13: 14 residues within 4Å: Chain A: N.128, T.181, S.182, W.183, F.226, I.228, Y.234 Chain E: D.69, V.70, I.71, W.90, R.92, Y.153, R.196 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:I.71, E:W.90, E:R.92, A:W.183, A:F.226, A:Y.234 pi-Cation interactions: E:R.92, E:R.92 CWB.17: 14 residues within 4Å: Chain A: D.69, V.70, I.71, W.90, R.92, Y.153, R.196 Chain B: N.128, T.181, S.182, W.183, F.226, I.228, Y.234 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.71, A:W.90, A:R.92, B:W.183, B:F.226, B:Y.234 pi-Cation interactions: A:R.92, A:R.92 CWB.20: 14 residues within 4Å: Chain B: D.69, V.70, I.71, W.90, R.92, Y.153, R.196 Chain C: N.128, T.181, S.182, W.183, F.226, I.228, Y.234 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:W.183, C:F.226, C:Y.234, B:I.71, B:I.71, B:W.90, B:R.92 pi-Cation interactions: B:R.92, B:R.92 CWB.23: 14 residues within 4Å: Chain C: D.69, V.70, I.71, W.90, R.92, Y.153, R.196 Chain D: N.128, T.181, S.182, W.183, F.226, I.228, Y.234 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.71, C:I.71, C:W.90, C:R.92, D:W.183, D:F.226, D:Y.234 pi-Cation interactions: C:R.92, C:R.92 CWB.24: 14 residues within 4Å: Chain D: D.69, V.70, I.71, W.90, R.92, Y.153, R.196 Chain E: N.128, T.181, S.182, W.183, F.226, I.228, Y.234 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:W.183, E:F.226, E:Y.234, D:I.71, D:W.90, D:R.92 pi-Cation interactions: D:R.92, D:R.92

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basak, S. et al., Molecular mechanism of setron-mediated inhibition of full-length 5-HT3Areceptor. Nat Commun (2019)

Release Date

2019-07-24

Peptides

5-hydroxytryptamine receptor 3A: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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5-hydroxytryptamine receptor 3A